In vitro studies of sequence-specific DNA-protein interactions using techniques where long DNA molecules is needed are currently limited by the size of synthesized DNA molecules, or is restricted to the commercially available DNA. For single molecule DNA imaging techniques using for instance nanochannels confinement, the small sized molecules make the interactions difficult to detect. The commercially available DNA, on the other hand, does not allow any freedom in choosing or changing the DNA sequence. Therefore, a method for producing long DNA molecules containing a sequence of choice would alleviate these limitations and greatly improve the possibility to study DNA-protein interactions.
The general concept of this paper was to create long, double-stranded DNA molecules with a sequence that is specifically designed to interact with the protein internal host factor. To make such molecules, three experimental procedures were developed, building on the single-stranded DNA products from a rolling circle amplification (RCA) reaction. The first experimental procedure was based on the presumed perfect annealing of smaller complementary strands to the single-stranded RCA product. The second experiment assumed that single-stranded gaps would be present in the duplex after annealing, hence the addition of a polymerisation reaction. In the third experiment, the RCA was run for 24 hours, to allow double-stranded product to be formed in the RCA.
The DNA strands were visualized using fluorescence microscopy, with the goal of studying them and their protein interactions in nanochannels. To be able to use this detection method, an external fluorescent dye, YOYO, is used in the main aim of the project. However, as these types of dyes change the native structure of DNA, an extra aim was to use the fluorescent base analogue tC incorporated into one of the duplex strands, leaving the native structure intact.
All three experimental procedures were shown to be capable of producing apparently double-stranded DNA molecules, that were larger than 100 kilo-base pairs albeit with a broad size distribution. This shows that the main aim in terms of procuing DNA molecules has been completed. The tC-containing DNA molecules were not visible under the microscope with the settings used, but appears to be promising.

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BibTeX @mastersthesis{Dekoning2018,author={Dekoning, Nora},title={A Rolling Circle Amplification-Based Methodology for Making Long, SequenceRepeating, DNA Duplexes},abstract={In vitro studies of sequence-specific DNA-protein interactions using techniques where long DNA molecules is needed are currently limited by the size of synthesized DNA molecules, or is restricted to the commercially available DNA. For single molecule DNA imaging techniques using for instance nanochannels confinement, the small sized molecules make the interactions difficult to detect. The commercially available DNA, on the other hand, does not allow any freedom in choosing or changing the DNA sequence. Therefore, a method for producing long DNA molecules containing a sequence of choice would alleviate these limitations and greatly improve the possibility to study DNA-protein interactions.
The general concept of this paper was to create long, double-stranded DNA molecules with a sequence that is specifically designed to interact with the protein internal host factor. To make such molecules, three experimental procedures were developed, building on the single-stranded DNA products from a rolling circle amplification (RCA) reaction. The first experimental procedure was based on the presumed perfect annealing of smaller complementary strands to the single-stranded RCA product. The second experiment assumed that single-stranded gaps would be present in the duplex after annealing, hence the addition of a polymerisation reaction. In the third experiment, the RCA was run for 24 hours, to allow double-stranded product to be formed in the RCA.
The DNA strands were visualized using fluorescence microscopy, with the goal of studying them and their protein interactions in nanochannels. To be able to use this detection method, an external fluorescent dye, YOYO, is used in the main aim of the project. However, as these types of dyes change the native structure of DNA, an extra aim was to use the fluorescent base analogue tC incorporated into one of the duplex strands, leaving the native structure intact.
All three experimental procedures were shown to be capable of producing apparently double-stranded DNA molecules, that were larger than 100 kilo-base pairs albeit with a broad size distribution. This shows that the main aim in terms of procuing DNA molecules has been completed. The tC-containing DNA molecules were not visible under the microscope with the settings used, but appears to be promising. },year={2018},note={62},}

RefWorks RT GenericSR ElectronicID 256240A1 Dekoning, NoraT1 A Rolling Circle Amplification-Based Methodology for Making Long, SequenceRepeating, DNA DuplexesYR 2018AB In vitro studies of sequence-specific DNA-protein interactions using techniques where long DNA molecules is needed are currently limited by the size of synthesized DNA molecules, or is restricted to the commercially available DNA. For single molecule DNA imaging techniques using for instance nanochannels confinement, the small sized molecules make the interactions difficult to detect. The commercially available DNA, on the other hand, does not allow any freedom in choosing or changing the DNA sequence. Therefore, a method for producing long DNA molecules containing a sequence of choice would alleviate these limitations and greatly improve the possibility to study DNA-protein interactions.
The general concept of this paper was to create long, double-stranded DNA molecules with a sequence that is specifically designed to interact with the protein internal host factor. To make such molecules, three experimental procedures were developed, building on the single-stranded DNA products from a rolling circle amplification (RCA) reaction. The first experimental procedure was based on the presumed perfect annealing of smaller complementary strands to the single-stranded RCA product. The second experiment assumed that single-stranded gaps would be present in the duplex after annealing, hence the addition of a polymerisation reaction. In the third experiment, the RCA was run for 24 hours, to allow double-stranded product to be formed in the RCA.
The DNA strands were visualized using fluorescence microscopy, with the goal of studying them and their protein interactions in nanochannels. To be able to use this detection method, an external fluorescent dye, YOYO, is used in the main aim of the project. However, as these types of dyes change the native structure of DNA, an extra aim was to use the fluorescent base analogue tC incorporated into one of the duplex strands, leaving the native structure intact.
All three experimental procedures were shown to be capable of producing apparently double-stranded DNA molecules, that were larger than 100 kilo-base pairs albeit with a broad size distribution. This shows that the main aim in terms of procuing DNA molecules has been completed. The tC-containing DNA molecules were not visible under the microscope with the settings used, but appears to be promising. LA engLK http://publications.lib.chalmers.se/records/fulltext/256240/256240.pdfOL 30